Why must a purine pair with a pyrimidine?

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Pairing of a specific purine to a specific pyrimidine is due to the structure and properties of each ring and the three-dimensional fit between complements. Purine and pyrimidine are organic, aromatic ring compounds that act as the building blocks of nucleic acid. In DNA, purines occur as adenine and guanine, while pyrimidines occur as thymine and cytosine. In DNA base pairing, adenine pairs with thymine, and guanine pairs with cytosine.

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Matching base pairs composed of one purine and one pyrimidine form hydrogen bonds. Purines have a double ring structure, and pyrimidines have a single ring structure. Adenine and thymine both have two sites where they form hydrogen bonds to each other, while guanine and cytosine have three sites. Bonded together, these nitrogenous bases form the rungs of the DNA ladder, or double helix.

The hydrogen bonding between rings is only possible in specific tautomeric form. As explained by the University of Maine’s Department of Chemistry, tautomers are isomers related by the changing position of a single hydrogen and a double bond. For each of the four nitrogenous bases, a specific tautomeric form must be incorporated for proper bonding, stability and attachment to the sugar-phosphate backbone of DNA. If the base pairs are the rungs of a ladder, the sugar-phosphate backbone acts as the sides of the ladder. With a helical twist of the ladder, there is less steric hindrance between neighboring atoms in the DNA molecule.